New Class Of HIV Drugs From Scripps Research?

To accomplish this goal, the team procured a “library” of 384
compound fragments that had been compiled by a company called
Active Sight. Screening fragments rather than larger compounds has
become more popular over the last several years, Perryman
explained, since using these smaller pieces is a more efficient way
to find promising structures than using libraries of large
compounds. In addition, fragments can be extended, combined, and
modified using “structure-based drug design” in a way that makes
them fit tightly into the right binding sites, without displaying
the unwanted interactions that sometimes come with larger
molecules. Using libraries of much larger, “lead-like” compounds is
less efficient, and those large compounds are less extendable.

Since the HIV protease molecule is in constant motion, the team
of scientists, which included members of Scripps Research Professor
John Elder’s lab, first crystallized the molecule in various
different conformations. The scientists then screened a library of
fragments against these crystals to see if any of them bound and
characterized the structural features of the results using the
Stanford Synchrotron Radiation Lightsource (SSRL). Stout notes
that, in total, the project conducted a massive screen of more than
800 crystals producing more than 400 data sets, a feat made
possible by SSRL’s robotic capabilities.

In their initial experiments, the scientists met with partial
success—enough to establish a proof-of-concept—as one fragment
attached to the “eye site” between the tip of a flap and the top of
the active site’s wall. However, the large active site of the
molecule tended to be problematic, interfering with the scientists’
goal of searching for fragments that bind to alternate sites on the
molecule.

To overcome this problem, the team “plugged up” the active site
with a known inhibitor so that the screen would identify only
fragments that bound to other regions of the protease. Perryman
noted that this innovative protocol could be applied to similar
work on many different disease-causing agents, especially those
that have developed drug resistance.

Using the new method for crystallographic screening, the team
found two “hits”—fragments 2-methylcyclohexanol and
indole-6-carboxylic acid. The scientists used additional x-ray
crystallographic experiments to confirm first that the fragments
indeed bound to novel sites in the protease and second that these
fragments change the structural preferences of protease.

“Since these fragments are very small, we wouldn’t expect them
to be potent inhibitors by themselves,” said Perryman. “But it’s
the beginning of a process where we can try to use these little
fragments to build up to a real potent inhibitor. The study
validates our predictions and lays the structural foundation for
the development of new classes of anti-AIDS drugs.”

Perryman and his colleagues in the Olson lab have been
using FightAIDS@Home, a computer modeling project dedicated to
finding new AIDS therapies in the face of evolving drug resistance,
to extend the work. FightAIDS@Home uses the massive computational
power of IBM’s “World Community Grid,” a global community of
Internet users who donate unused time on their personal computers
for projects that benefit humanity. For more information on the
project and how to participate, visit
http://fightaidsathome.scripps.edu/ or
http://www.worldcommunitygrid.org/.

In addition to Perryman, Stout, Olson, and Elder, authors of the
paper, “Fragment-Based Screen against HIV Protease,” are Qing Zhang
of Scripps Research and GlaxoSmithKline, Holly H. Soutter of
Scripps Research and Pfizer Global Research and Development, Robin
Rosenfeld of Scripps Research and Active Sight, and Duncan E. McRee
of Active Sight and Sorrento Technologies. See
http://www3.interscience.wiley.com/journal/123244298/abstract

The research was supported by “program project” grant P01
GM0833658 from the National Institutes of Health. SSRL is a
national user facility operated by Stanford University on behalf of
the U.S. Department of Energy.